Import data

Doublets were removed and clonotypes were selected by “1 alpha and 1 beta chain”.

Fig H

Clonotypes were filtered by “1 alpha and 1 beta chain”

M6 Clonotype Distribution

Table
Clonotypes : ones with 1 alpha and 1 beta chain

##   Sample Frequency_of_clonotype number
## 1     M6              freq >= 5      0
## 2     M6          2 <= freq < 5      8
## 3     M6               freq = 1   1111
## 4     M6                  total   1119

M7 Clonotype Distribution

Table
Clonotypes : ones with 1 alpha and 1 beta chain

##   Sample Frequency_of_clonotype number
## 1     M7              freq >= 5      0
## 2     M7          2 <= freq < 5     22
## 3     M7               freq = 1   1186
## 4     M7                  total   1208

Clustering

Cluster based on the resolutions

resolution_values <- c(0.2, 0.4, 0.8, 1)

Clusters with the different resolutions

Find markers

Markers based on clustering-resolutions : 0.2, 0.4, 0.8, 1

Marker genes

resolution 0.2

Download cluster marker file

## [1] "RNA_snn_res.0.2"

resolution 0.4

Download cluster marker file

## [1] "RNA_snn_res.0.4"

resolution 0.8

Download cluster marker file

## [1] "RNA_snn_res.0.8"

resolution 1

Download cluster marker file

## [1] "RNA_snn_res.1"



Cluster annotation



You can annotate each cluster using the table provided below.

## [1] "RNA_snn_res.0.2"



You can annotate each cluster using the table provided below.

## [1] "RNA_snn_res.0.4"



You can annotate each cluster using the table provided below.

## [1] "RNA_snn_res.0.8"



You can annotate each cluster using the table provided below.

## [1] "RNA_snn_res.1"



Recolor UMAP with resolution 0.2 clustering and annotation

##      cluster                Annotation   color
## 1   cluster0                      MDSC #28B463
## 2   cluster1                Neutrophil #3482DB
## 3   cluster2          Monocyte related #5CD3F6
## 4   cluster3                    T cell #FA8072
## 5   cluster4            Red blood cell #F65CCC
## 6   cluster5                    B cell #9C640C
## 7   cluster6            Red blood cell #F65CCC
## 8   cluster7                   NK cell #8E44AD
## 9   cluster8 Macrophage/Dendritic cell #FF9033
## 10  cluster9                  Basophil #1A5276
## 11 cluster10                           #FDFEFE